supervisely 6.73.360__tar.gz → 6.73.362__tar.gz

{supervisely-6.73.360/supervisely.egg-info → supervisely-6.73.362}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: supervisely
-Version: 6.73.360
+Version: 6.73.362
 Summary: Supervisely Python SDK.
 Home-page: https://github.com/supervisely/supervisely
 Author: Supervisely

{supervisely-6.73.360 → supervisely-6.73.362}/supervisely/nn/inference/inference.py

@@ -1519,7 +1519,7 @@ class Inference:
         if frames_count is not None:
             n_frames = frames_count
         elif end_frame_index is not None:
-            n_frames = end_frame_index - start_frame_index
+            n_frames = end_frame_index - start_frame_index + 1
         elif duration is not None:
             fps = frames_reader.fps()
             n_frames = int(duration * fps)
@@ -1729,7 +1729,6 @@ class Inference:
         inference_settings = self._get_inference_settings(state)
         logger.debug(f"Inference settings:", extra=inference_settings)
         batch_size = self._get_batch_size_from_state(state)
-        video_id = state["videoId"]
         video_id = get_value_for_keys(state, ["videoId", "video_id"], ignore_none=True)
         if video_id is None:
             raise ValueError("Video id is not provided")

{supervisely-6.73.360 → supervisely-6.73.362}/supervisely/project/download.py

@@ -409,12 +409,22 @@ def _project_meta_changed(meta1: ProjectMeta, meta2: ProjectMeta) -> bool:
     return False
 
 
+def _get_ds_full_name(
+    dataset_info: DatasetInfo, all_ds_infos: List[DatasetInfo], suffix: str = ""
+) -> str:
+    if dataset_info.parent_id is None:
+        return dataset_info.name + suffix
+    parent = next((ds_info for ds_info in all_ds_infos if ds_info.id == dataset_info.parent_id))
+    return _get_ds_full_name(parent, all_ds_infos, "/" + dataset_info.name)
+
+
 def _validate_dataset(
     api: Api,
     project_id: int,
     project_type: str,
     project_meta: ProjectMeta,
     dataset_info: DatasetInfo,
+    all_ds_infos: List[DatasetInfo] = None,
 ):
     try:
         project_class = get_project_class(project_type)
@@ -430,10 +440,12 @@ def _validate_dataset(
     except:
         logger.debug("Validating dataset failed. Unable to download items infos.", exc_info=True)
         return False
+    if all_ds_infos is None:
+        all_ds_infos = api.dataset.get_list(project_id, recursive=True)
     project_meta_changed = _project_meta_changed(project_meta, project.meta)
     for dataset in project.datasets:
         dataset: Dataset
-        if dataset.name.endswith(dataset_info.name):  # TODO: fix it later
+        if dataset.name == _get_ds_full_name(dataset_info, all_ds_infos):
             diff = set(items_infos_dict.keys()).difference(set(dataset.get_items_names()))
             if diff:
                 logger.debug(
@@ -481,7 +493,11 @@ def _validate_dataset(
 
 
 def _validate(
-    api: Api, project_info: ProjectInfo, project_meta: ProjectMeta, dataset_infos: List[DatasetInfo]
+    api: Api,
+    project_info: ProjectInfo,
+    project_meta: ProjectMeta,
+    dataset_infos: List[DatasetInfo],
+    all_ds_infos: List[DatasetInfo] = None,
 ):
     project_id = project_info.id
     to_download, cached = _split_by_cache(
@@ -498,6 +514,7 @@ def _validate(
             project_info.type,
             project_meta,
             dataset_info,
+            all_ds_infos,
         ):
             to_download.add(ds_path)
             cached.remove(ds_path)
@@ -520,7 +537,7 @@ def _add_save_items_infos_to_kwargs(kwargs: dict, project_type: str):
 
 
 def _add_resume_download_to_kwargs(kwargs: dict, project_type: str):
-    supported_force_projects = (str(ProjectType.IMAGES),)
+    supported_force_projects = (str(ProjectType.IMAGES), (str(ProjectType.VIDEOS)))
     if project_type in supported_force_projects:
         kwargs["resume_download"] = True
     return kwargs
@@ -592,13 +609,14 @@ def download_to_cache(
     project_meta = ProjectMeta.from_json(api.project.get_meta(project_id))
     if dataset_infos is not None and dataset_ids is not None:
         raise ValueError("dataset_infos and dataset_ids cannot be specified at the same time")
+    all_ds_infos = api.dataset.get_list(project_id, recursive=True)
     if dataset_infos is None:
         if dataset_ids is None:
-            dataset_infos = api.dataset.get_list(project_id, recursive=True)
+            dataset_infos = all_ds_infos
         else:
-            dataset_infos = [api.dataset.get_info_by_id(dataset_id) for dataset_id in dataset_ids]
+            dataset_infos = [ds_info for ds_info in all_ds_infos if ds_info.id in dataset_ids]
     path_to_info = {_get_dataset_path(api, dataset_infos, info.id): info for info in dataset_infos}
-    to_download, cached = _validate(api, project_info, project_meta, dataset_infos)
+    to_download, cached = _validate(api, project_info, project_meta, dataset_infos, all_ds_infos)
     if progress_cb is not None:
         cached_items_n = sum(path_to_info[ds_path].items_count for ds_path in cached)
         progress_cb(cached_items_n)

{supervisely-6.73.360 → supervisely-6.73.362}/supervisely/project/video_project.py

@@ -16,7 +16,7 @@ from supervisely.api.dataset_api import DatasetInfo
 from supervisely.api.module_api import ApiField
 from supervisely.api.video.video_api import VideoInfo
 from supervisely.collection.key_indexed_collection import KeyIndexedCollection
-from supervisely.io.fs import mkdir, touch, touch_async
+from supervisely.io.fs import clean_dir, mkdir, touch, touch_async
 from supervisely.io.json import dump_json_file, dump_json_file_async, load_json_file
 from supervisely.project.project import Dataset, OpenMode, Project
 from supervisely.project.project import read_single_project as read_project_wrapper
@@ -1056,6 +1056,7 @@ class VideoProject(Project):
         save_video_info: bool = False,
         log_progress: bool = True,
         progress_cb: Optional[Union[tqdm, Callable]] = None,
+        resume_download: Optional[bool] = False,
     ) -> None:
         """
         Download video project from Supervisely to the given directory.
@@ -1109,6 +1110,7 @@ class VideoProject(Project):
             save_video_info=save_video_info,
             log_progress=log_progress,
             progress_cb=progress_cb,
+            resume_download=resume_download,
         )
 
     @staticmethod
@@ -1182,6 +1184,7 @@ class VideoProject(Project):
         log_progress: bool = True,
         progress_cb: Optional[Union[tqdm, Callable]] = None,
         include_custom_data: bool = False,
+        resume_download: Optional[bool] = False,
         **kwargs,
     ) -> None:
         """
@@ -1238,6 +1241,7 @@ class VideoProject(Project):
             log_progress=log_progress,
             progress_cb=progress_cb,
             include_custom_data=include_custom_data,
+            resume_download=resume_download,
             **kwargs,
         )
 
@@ -1252,6 +1256,7 @@ def download_video_project(
     log_progress: bool = True,
     progress_cb: Optional[Union[tqdm, Callable]] = None,
     include_custom_data: Optional[bool] = False,
+    resume_download: Optional[bool] = False,
 ) -> None:
     """
     Download video project to the local directory.
@@ -1312,9 +1317,22 @@ def download_video_project(
     LOG_BATCH_SIZE = 1
 
     key_id_map = KeyIdMap()
-    project_fs = VideoProject(dest_dir, OpenMode.CREATE)
-    meta = ProjectMeta.from_json(api.project.get_meta(project_id))
+
+    meta = ProjectMeta.from_json(api.project.get_meta(project_id, with_settings=True))
+    if os.path.exists(dest_dir) and resume_download:
+        dump_json_file(meta.to_json(), os.path.join(dest_dir, "meta.json"))
+        try:
+            project_fs = VideoProject(dest_dir, OpenMode.READ)
+        except RuntimeError as e:
+            if "Project is empty" in str(e):
+                clean_dir(dest_dir)
+                project_fs = None
+            else:
+                raise
+    if project_fs is None:
+        project_fs = VideoProject(dest_dir, OpenMode.CREATE)
     project_fs.set_meta(meta)
+
     if progress_cb is not None:
         log_progress = False
 
@@ -1549,6 +1567,7 @@ async def download_video_project_async(
     log_progress: bool = True,
     progress_cb: Optional[Union[tqdm, Callable]] = None,
     include_custom_data: Optional[bool] = False,
+    resume_download: Optional[bool] = False,
     **kwargs,
 ) -> None:
     """
@@ -1603,9 +1622,19 @@ async def download_video_project_async(
 
     key_id_map = KeyIdMap()
 
-    project_fs = VideoProject(dest_dir, OpenMode.CREATE)
-
-    meta = ProjectMeta.from_json(api.project.get_meta(project_id))
+    meta = ProjectMeta.from_json(api.project.get_meta(project_id, with_settings=True))
+    if os.path.exists(dest_dir) and resume_download:
+        dump_json_file(meta.to_json(), os.path.join(dest_dir, "meta.json"))
+        try:
+            project_fs = VideoProject(dest_dir, OpenMode.READ)
+        except RuntimeError as e:
+            if "Project is empty" in str(e):
+                clean_dir(dest_dir)
+                project_fs = None
+            else:
+                raise
+    if project_fs is None:
+        project_fs = VideoProject(dest_dir, OpenMode.CREATE)
     project_fs.set_meta(meta)
 
     if progress_cb is not None:

{supervisely-6.73.360 → supervisely-6.73.362}/supervisely/volume/volume.py

@@ -9,9 +9,11 @@ import numpy as np
 import pydicom
 import SimpleITK as sitk
 import stringcase
+from trimesh import Trimesh
 
 import supervisely.volume.nrrd_encoder as nrrd_encoder
 from supervisely import logger
+from supervisely.geometry.mask_3d import Mask3D
 from supervisely.io.fs import get_file_ext, get_file_name, list_files_recursively
 
 # Do NOT use directly for extension validation. Use is_valid_ext() /  has_valid_ext() below instead.
@@ -783,7 +785,7 @@ def convert_nifti_to_nrrd(path: str) -> Tuple[np.ndarray, dict]:
         data, header = sly.volume.convert_nifti_to_nrrd(path)
     """
 
-    import nibabel as nib # pylint: disable=import-error
+    import nibabel as nib  # pylint: disable=import-error
 
     nifti = nib.load(path)
     reordered_to_ras_nifti = nib.as_closest_canonical(nifti)
@@ -799,6 +801,7 @@ def convert_nifti_to_nrrd(path: str) -> Tuple[np.ndarray, dict]:
     }
     return data, header
 
+
 def convert_3d_nifti_to_nrrd(path: str) -> Tuple[np.ndarray, dict]:
     """Convert 3D NIFTI volume to NRRD format.
     Volume automatically reordered to RAS orientation as closest to canonical.
@@ -830,14 +833,14 @@ def convert_3d_nifti_to_nrrd(path: str) -> Tuple[np.ndarray, dict]:
     space_directions = (direction.T * spacing[:, None]).tolist()
 
     header = {
-            "dimension": 3,
-            "space": "right-anterior-superior",
-            "sizes": list(data.shape),
-            "space directions": space_directions,
-            "endian": "little",
-            "encoding": "gzip",
-            "space origin": origin
-        }
+        "dimension": 3,
+        "space": "right-anterior-superior",
+        "sizes": list(data.shape),
+        "space directions": space_directions,
+        "endian": "little",
+        "encoding": "gzip",
+        "space origin": origin,
+    }
     return data, header
 
 
@@ -861,3 +864,96 @@ def is_nifti_file(path: str) -> bool:
         return True
     except nib.filebasedimages.ImageFileError:
         return False
+
+
+def convert_3d_geometry_to_mesh(
+    geometry: Mask3D,
+    spacing: tuple = None,
+    level: float = 0.5,
+    apply_decimation: bool = False,
+    decimation_fraction: float = 0.5,
+) -> Trimesh:
+    """
+    Converts a 3D geometry (Mask3D) to a Trimesh mesh.
+
+    :param geometry: The 3D geometry to convert.
+    :type geometry: supervisely.geometry.mask_3d.Mask3D
+    :param spacing: Voxel spacing in (x, y, z). Default is taken from geometry meta.
+    :type spacing: tuple
+    :param level: Isosurface value for marching cubes. Default is 0.5.
+    :type level: float
+    :param apply_decimation: Whether to simplify the mesh. Default is False.
+    :type apply_decimation: bool
+    :param decimation_fraction: Fraction of faces to keep if decimation is applied. Default is 0.5.
+    :type decimation_fraction: float
+    :return: The resulting Trimesh mesh.
+    :rtype: trimesh.Trimesh
+
+    :Usage example:
+
+        .. code-block:: python
+
+            mask3d = Mask3D.create_from_file("path/to/mask3d")
+            mesh = convert_3d_geometry_to_mesh(mask3d, spacing=(1.0, 1.0, 1.0), level=0.7, apply_decimation=True)
+    """
+    from skimage import measure
+
+    # Flip the mask along the x-axis to correct mirroring
+    mask = np.flip(geometry.data, axis=0)
+    if spacing is None:
+        try:
+            spacing = tuple(
+                float(abs(direction[i])) for i, direction in enumerate(geometry._space_directions)
+            )
+        except Exception as e:
+            logger.warning(
+                "Failed to get spacing from geometry meta. Using (1.0, 1.0, 1.0).", exc_info=1
+            )
+            spacing = (1.0, 1.0, 1.0)
+
+    # marching_cubes expects (z, y, x) order
+    verts, faces, normals, _ = measure.marching_cubes(
+        mask.astype(np.float32), level=level, spacing=spacing
+    )
+    mesh = Trimesh(vertices=verts, faces=faces, vertex_normals=normals, process=False)
+
+    if apply_decimation and 0 < decimation_fraction < 1:
+        mesh = mesh.simplify_quadric_decimation(int(len(mesh.faces) * decimation_fraction))
+
+    return mesh
+
+
+def export_3d_as_mesh(geometry: Mask3D, output_path: str, kwargs=None):
+    """
+    Exports the 3D mesh representation of the object to a file in either STL or OBJ format.
+
+    :param geometry: The 3D geometry to be exported.
+    :type geometry: supervisely.geometry.mask_3d.Mask3D
+    :param output_path: The path to the output file. Must have a ".stl" or ".obj" extension.
+    :type output_path: str
+    :param kwargs: Additional keyword arguments for mesh generation. Supported keys:
+        - spacing (tuple): Voxel spacing in (x, y, z). By default the value will be taken from geometry meta.
+        - level (float): Isosurface value for marching cubes. Default is 0.5.
+        - apply_decimation (bool): Whether to simplify the mesh. Default is False.
+        - decimation_fraction (float): Fraction of faces to keep if decimation is applied. Default is 0.5.
+    :type kwargs: dict, optional
+    :return: None
+
+    :Usage example:
+
+        .. code-block:: python
+
+        mask3d_path = "path/to/mask3d"
+        mask3d = Mask3D.create_from_file(mask3d_path)
+
+        mask3d.export_3d_as_mesh(mask3d, "output.stl", {"spacing": (1.0, 1.0, 1.0), "level": 0.7, "apply_decimation": True})
+    """
+
+    if kwargs is None:
+        kwargs = {}
+
+    if get_file_ext(output_path).lower() not in [".stl", ".obj"]:
+        raise ValueError('File extension must be either ".stl" or ".obj"')
+
+    mesh = convert_3d_geometry_to_mesh(geometry, **kwargs)
+    mesh.export(output_path)

{supervisely-6.73.360 → supervisely-6.73.362}/supervisely/volume_annotation/volume_annotation.py

@@ -11,6 +11,7 @@ from supervisely.volume_annotation.volume_figure import VolumeFigure
 
 from supervisely.project.project_meta import ProjectMeta
 from supervisely._utils import take_with_default
+from supervisely.io.fs import file_exists
 from supervisely.video_annotation.key_id_map import KeyIdMap
 from supervisely.volume_annotation.slice import Slice
 from supervisely.volume_annotation.volume_tag_collection import VolumeTagCollection
@@ -30,7 +31,7 @@ from supervisely.volume_annotation.constants import (
     PLANES,
     SPATIAL_FIGURES,
 )
-
+from supervisely.io.fs import get_file_name
 from supervisely.io.json import dump_json_file
 
 
@@ -484,7 +485,13 @@ class VolumeAnnotation:
         )
 
     @classmethod
-    def from_json(cls, data: dict, project_meta: ProjectMeta, key_id_map: KeyIdMap = None):
+    def from_json(
+        cls,
+        data: dict,
+        project_meta: ProjectMeta,
+        key_id_map: KeyIdMap = None,
+        spatial_geometry_paths: Union[list, dict] = None,
+    ):
         """
         Convert a json dict to VolumeAnnotation.
 
@@ -494,6 +501,11 @@ class VolumeAnnotation:
         :type project_meta: ProjectMeta
         :param key_id_map: KeyIdMap object.
         :type key_id_map: KeyIdMap, optional
+        :param spatial_geometry_paths: Optional. Can be either:
+            - a list of file paths to spatial geometry files, where each file name should match either the figure's id or the hex value of its key,
+            - or a dict mapping figure ids (or keys) to their corresponding geometry file paths.
+            Used to load 3D geometry for spatial figures.
+        :type spatial_geometry_paths: list or dict, optional
         :return: VolumeAnnotation object
         :rtype: :class:`VolumeAnnotation<VolumeAnnotation>`
         :Usage example:
@@ -585,6 +597,31 @@ class VolumeAnnotation:
                 slice_index=None,
                 key_id_map=key_id_map,
             )
+            if spatial_geometry_paths:
+                figure_id = figure_json["id"]
+                if isinstance(spatial_geometry_paths, list):
+                    spatial_geometry_paths = {
+                        get_file_name(path): path for path in spatial_geometry_paths
+                    }
+                    geometry_path = spatial_geometry_paths.get(
+                        figure.key().hex
+                    ) or spatial_geometry_paths.get(str(figure_id))
+                elif isinstance(spatial_geometry_paths, dict):
+                    geometry_path = spatial_geometry_paths.get(figure_id, None)
+                else:
+                    raise ValueError(
+                        f"spatial_geometry_paths should be either a list or a dict. Got: {type(spatial_geometry_paths)}"
+                    )
+
+                if geometry_path is not None:
+                    if not file_exists(geometry_path):
+                        raise RuntimeError(
+                            f"Geometry file {geometry_path} for figure {figure_id} does not exist."
+                        )
+                    mask3d = Mask3D.create_from_file(geometry_path)
+                    mask3d.sly_id = figure_id
+                    figure._set_3d_geometry(mask3d)
+
             spatial_figures.append(figure)
 
         return cls(

{supervisely-6.73.360 → supervisely-6.73.362}/supervisely/volume_annotation/volume_figure.py

@@ -1,28 +1,30 @@
 # coding: utf-8
 from __future__ import annotations
+
 import uuid
-from typing import Union, Optional, Literal
-from numpy import ndarray
+from typing import Literal, Optional, Union
 from uuid import UUID
-from supervisely.video_annotation.video_figure import VideoFigure
-from supervisely.video_annotation.key_id_map import KeyIdMap
-from supervisely.geometry.closed_surface_mesh import ClosedSurfaceMesh
-from supervisely.geometry.mask_3d import Mask3D
+
+from numpy import ndarray
+
+import supervisely.volume_annotation.constants as constants
+from supervisely._utils import take_with_default
+from supervisely.annotation.json_geometries_map import GET_GEOMETRY_FROM_STR
 from supervisely.api.module_api import ApiField
 from supervisely.geometry.any_geometry import AnyGeometry
-from supervisely.annotation.json_geometries_map import GET_GEOMETRY_FROM_STR
-from supervisely._utils import take_with_default
-from supervisely.volume_annotation.volume_object import VolumeObject
-from supervisely.geometry.geometry import Geometry
-import supervisely.volume_annotation.constants as constants
-from supervisely.volume_annotation.constants import ID, KEY, OBJECT_ID, OBJECT_KEY, META
+from supervisely.geometry.closed_surface_mesh import ClosedSurfaceMesh
 from supervisely.geometry.constants import (
+    CLASS_ID,
+    CREATED_AT,
     LABELER_LOGIN,
     UPDATED_AT,
-    CREATED_AT,
-    CLASS_ID,
 )
-
+from supervisely.geometry.geometry import Geometry
+from supervisely.geometry.mask_3d import Mask3D
+from supervisely.video_annotation.key_id_map import KeyIdMap
+from supervisely.video_annotation.video_figure import VideoFigure
+from supervisely.volume_annotation.constants import ID, KEY, META, OBJECT_ID, OBJECT_KEY
+from supervisely.volume_annotation.volume_object import VolumeObject
 from supervisely.volume_annotation.volume_object_collection import (
     VolumeObjectCollection,
 )

{supervisely-6.73.360 → supervisely-6.73.362/supervisely.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: supervisely
-Version: 6.73.360
+Version: 6.73.362
 Summary: Supervisely Python SDK.
 Home-page: https://github.com/supervisely/supervisely
 Author: Supervisely